Colin L. Stark - HTG(A)A 2024
Bio-engineered Recycling, Ore Processing, and Manufacturing
Inspired by Karishwaralal et al (2009) (DOI: 10.1016/j.biortech.2009.05.051) and Dietrich et al. (2021) (DOI: 10.1038/s41467-021-24796-0).
This project is a vision of biological ore processing, recycling, and manufacturing using microbial systems. There are well known challenges to breaking down the detritus found in landfills, recycling centers, and junkyards. The composition of these materials is mixed, containing compounds which are toxic to many species. Hydrocarbons and biological matter can be broken apart using more traditional methods and more common bacteria but covering the rest of the periodic table has proven difficult.
Hundreds of species of bacteria and archaea have been found to consume metals and strongly-bonded atoms within the molecules often found in the waste stream of modern society. Recently, the Arnold Lab at Caltech published work showing that directed evolution could be used to produce enzymes which break Carbon Silicon bonds (DOI: 10.1126/science.adi555). Other bacteria naturally break down such materials. Shewanella oneidensis and Geobacter sulfurreducens reduce heavy metals, removing them from solution. Cupriavidus metallidurans likewise removes gold from gold chloride and produces metallic gold. Fungi such as Aspergillus niger dissolve metals using organic acids. Another, Penicillium simplicissimum, accumulates uranium from solution.
In anabolic terms, some variants of Bacillus licheniformis are able to process metal ions in solution and produce nanoscale metallic cubes. P. aeruginosa-14 has been found to produce R-bodies, coiled proteins which snap into a long cylindric shape in low pH solutions. These last two are examples of nanoscale building blocks which can potentially be used to rearrange matter mechanically, using catabolic process to break down waste and ore and anabolic process to build something new for macroscale use.
One application might be a 3D printed scaffold of agar seeded with smaller regions containing nutrients specific to P. aeruginosa-14 programmed to overproduce R-bodies (bypassing cell toxicity) or B. licheniformis which has been programmed to condense metal ions into solid cubes. The PA14 renders a framework of R-bodies which can be expanded or contracted based on local pH, which can be artificially appended with moieties which attach to surface proteins of specific cells, the BL renders a series of metal cubes acting as voxels which can be flash-welded to produce a solid metal macroscale objects. Variations on the method of R-body production can give be used to change the density and structure of the final product. R-bodys appended or prefixed by sequences which produce moieties specific to the outside of a B.licheniformis cell might be used, for example, to position the microbes in a grid which expands or contracts to vary arrangement of metal nanocubes based on local pH. Controlling the temperature, pH of the solution, as well as the concentration and distribution of nutrients may be able to change the properties of the final material.
Goals:
Dietrich et al. (2021) (DOI: https://doi.org/10.1038/s41467-021-24796-0)
Jessica Polka's electron micrograph of negatively stained type 51 in a low pH solution (Wikipedia)
Sourced from Addgene.org
A toy design which uses a similar expansion mechanism to R-bodies.
A toy design which uses a similar expansion mechanism to R-bodies.
Karishwaralal et al (2009) (DOI: 10.1016/j.biortech.2009.05.051)
SEM image of gold nanocubes fabricated by Bacillus licheniformis (from Kalishwaralal 2009)
The second component of this assignment is to develop a regulatory framework to keep this technology from being misused.
The regulation I envision would be licensure to prevent the organisms from being used outside the “safe sandbox” of a well planned GMP environment, recycling facility, or mining facility which is contractually designated. Customers would pay for a license to use the organisms, and they would be subject to regulations within that framework.
The organisms being used would also have a regulatory operon which prevents the expression of key sequences without a proprietary molecule being present in the nutrient supply, a molecule which is not present in significant quantities in Earth’s regolith, yet would be critical to colony growth. The use of this patented system would necessitate the purchase of the key molecule (KM), which is sold only to those with a license to use the product. Customers using the product would be required to consult with our company to design a solution which meets their needs without negative impact on the environment, and uses outside that scope could be monitored for potential harm and denied future sales if the circumstances
In Crichton’s Jurassic Park, lysine deficiency was used to ensure the animals could not survive outside the park. Lessons from fiction warn us to test our ability to control the whims of nature. It would likely be necessary to have more backups in place, such as a limit to the number of generations which could be produced from any one CFU produced from the original vial being sold. Annual audits of large-scale users and randomized inspections of small-scale users can be utilized to understand the market, report back to regulators, and adjust restrictions as needed. For equitable access, it could be useful to use the cost efficiency of selling at increased margins to local buyers to offset the cost of sale to international buyers in developing nations at near production costs, despite a higher cost to regulate and ensure contract compliance.
One major issue with this approach to processing is a lack of control over bacteria which are intended to be able to consume essentially any matter. These sorts of microbes would be very useful to criminal organizations attempting to destroy evidence of crimes and rogue nations attempting to eliminate enemy troops in a warzone. These are issues which techniques such as regulatory operons and programmed generational apoptosis might be able to solve, but which also necessitate some level of government-level response. While it may be possible to add laws and regulations with some level of enforcement, it is also expected that not everyone who writes those laws or enforces them will understand their importance. This is also why regulating from within the industry of biotechnology will be critical to being able to deploy next generation bioengineered organisms.